string getCommandName() { return "shhh.seqs"; }
string getCommandCategory() { return "Hidden"; }
string getHelpString();
+ string getCitation() { return "no citation"; }
+ string getDescription() { return "shhh.seqs"; }
+
int execute();
void help() { m->mothurOut(getHelpString()); }
int abort;
- string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName;
+ string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName, compositeNamesFileName;
int processors, maxIters;
float cutoff, sigma, minDelta;
vector<int> mapSeqToUnique;
vector<int> mapUniqueToSeq;
vector<int> uniqueLengths;
-
+
+ vector<string> outputNames;
+
int numSeqs, numUniques, numOTUs, numFlowCells;
void getSingleLookUp();